The model cyanobacterium Synechocystis sp. PCC 6803 is widely used in studies of photosynthesis, environmental sensing, and stress-response. Its capacity for straightforward genetic engineering and the early publication of its genome sequence meant that substrains of this organism have been dispersed widely among laboratories, particularly for the purposes of investigating the function of the water-splitting enzyme of photosynthesis, Photosystem II (PS II). Recently, advances in genome sequencing technology have revealed genomic divergence among these substrains, with a largely unknown level of resultant phenotypic variation. In this study, the capacity for Synechocystis sp. PCC 6803 wild types to undergo genomic change was analysed by assembly of the genome sequence of the ‘GT-O1’ and ‘GT-O2’ substrains in use at the University of Otago. In the GT-O1 substrain, a possible instance of active genome transposition processes involving a Tc1/mariner-type transposase-encoding gene was observed, and in the GT-O2 substrain a mutation detected in chlH was associated with a reduction in chlorophyll biosynthesis. It is suggested that long-term culture conditions induce genomic changes with major functional consequences in some wild-type substrains, in spite of theoretically ideal laboratory growth conditions. However, phenotypic analysis suggested that the GT-O1 substrain is comparable to other substrains of Synechocystis sp. PCC 6803 held overseas. The capacity for genome mutation in response to gene deletions affecting PS II was also analysed. Some strains carrying mutations in the extrinsic proteins or domains of PS II display an enigmatic pH 7.5-sensitive phenotype, but pH 7.5-growth of a ∆PsbO:∆PsbU strain could be rescued by genome mutations that apparently affect PS II-independent cellular processes. Assembly of the genome of a pH-insensitive ∆PsbO:∆PsbU pseudorevertant identified a mutation in pmgA that appears to affect carbon uptake, and accordingly CO2 enrichment rescued growth of some pH-sensitive PS II mutants, including the ∆PsbO:∆PsbU strain. To further investigate the effect of external pH on the membrane-embedded PS II complex, analysis of a pH-sensitive strain lacking PsbV and carrying a mutation in Loop E of the PS II core antenna CP47 protein revealed that mutations in the vicinity of the redox-active tyrosine YD appear to alter PS II redox equilibria. In a CP47 E364Q:∆PsbV mutant, the stability of YD+QA- charge pairs in PS II and possibly the capacity of YD to maintain charge equilibrium with the PS II oxygen-evolving complex was altered, likely contributing to pH-sensitivity. This suggests that pH affects PS II directly and indirectly, due to a complex interplay of pH effects on electron transport, carbon uptake, pH homeostasis, and PS II redox equilibria.